In this interview, NewsMedical talks to Jason Otterstrom in regards to the position of AI-based Athena Zebrafish software program in exploring Zebrafish imaging outcomes and its significance for bio-medical analysis utilizing Zebrafish fashions. Athena is now obtainable for obtain with a versatile pay-per-use license.
How can high-content imaging of Zebrafish revolutionize the bio-medical analysis area?
Zebrafish (Danio rerio) are a promising emergent mannequin system for biomedical analysis with the potential to allow quick, excessive throughput research of human illness in residing vertebrates.
Humans and zebrafish have many of the similar organs, share 70% of the identical genes, and 84% of the genes related to human illness have zebrafish counterparts.
Zebrafish embryos are clear and might be manipulated on the single-cell stage, then rapidly develop into larvae in a matter of days. This physiological growth might be imaged with a microscope utilizing hundreds of particular person fish to straight visualize the impact of remedies on organ techniques, growth and physiology.
No different well-characterized organic mannequin system is at present capable of supply these benefits.
Dr. Otterstrom: “We supply three inexpensive license packages for various throughput wants. With an efficient value between $0.15 and $0.29 USD per picture analyzed, any Zebrafish lab or researcher can use Athena software program to boost their evaluation workflows.” Image Credit: IDEA Bio-Medical Ltd.
How are photos of zebrafish used, and why are they essential for researchers?
Microscopy photos of zebrafish are analyzed to extract numerical or quantitative details about the embryos and larvae. The animal’s clear physique makes a lot of the fish’s inner anatomy observable, even with easy bright-field imaging.
Genetic manipulation permits the insertion of fluorescent proteins into the stay zebrafish for tissue-specific imaging and evaluation.
Life science researchers then analyze photos of zebrafish to review and measure organic and physiological modifications occurring in several anatomical areas inside a residing fish. For instance, organ growth and mobile proliferation or loss of life in relation to pharmacokinetics, toxicity, most cancers, and genetic modifications might be straight noticed and measured.
How can AI assist in these investigations?
Analyzing photos of zebrafish is a time-consuming bottleneck in screening research. While the pictures could also be simply interpretable by a human, typical picture evaluation algorithms don’t readily detect the fish or its anatomy. Instead, measurements are carried out manually utilizing single photos.
IDEA Bio-Medical discovered of this problem from our shoppers, so we created a novel deep-learning AI (synthetic intelligence) algorithm to robotically analyze their Zebrafish photos for them.
The AI coaching course of is advanced and error-prone, requiring substantial effort and time that our biology-focused shoppers couldn’t do themselves. The AI we have now developed can now robustly establish objects just like the zebrafish contour and its inner anatomy which are clearly seen to us people.
We now need to make this software obtainable to all zebrafish researchers, regardless of which microscope they use.
IDEA’s Zebrafish evaluation software program was developed with our shoppers, for our shoppers.
Athena software program permits parameter-free Zebrafish evaluation utilizing easy bright-field photos, extracting the fish contour and far of its inner anatomy (yolk sac, eye, notocord and extra), together with physique areas of the top, trunk, and tail. Image Credit: IDEA Bio-Medical Ltd.
Why do we want details about Zebrafish anatomy to interpret fluorescence alerts?
Many processes investigated utilizing zebrafish happen or start in particular organs or areas inside the physique. They might be marked with fluorescence labeling to picture the tissue or cells of curiosity. However, these have to be distinguished from undesired alerts and autofluorescence.
For instance, within the zebrafish larva, hematopoietic stem cells (HSC) originate in a selected space inside the tail – in any other case often known as the caudal hematopoietic tissue (CHT). It is analogous to the mammalian fetal liver and related to leukemia in people. Studies wanting on the proliferation of GFP-labeled HSC must focus particularly on the tail and ignore these fluorescent alerts current elsewhere, comparable to circulating cells and yolk sac autofluorescence.
Athena is at present the one software program obtainable that allows high-content screening on this context. It permits automated cell counts completely inside particular components of the fish to maximise each throughput and information extracted.
It contrasts widespread approaches, comparable to easy depth thresholding, which ignores the seen anatomy. Instead, all fluorescence is gathered collectively, regardless of its origin, producing noisy information. Manual choice of the tail would enhance high quality however severely restrict achievable throughput.
Athena is a first-of-its-kind automated picture evaluation software program devoted to zebrafish microscopy. Image Credit: IDEA Bio-Medical Ltd.
What is Athena picture evaluation software program, and the way can it’s used?
Athena Zebrafish is a stand-alone software program developed and provided by IDEA Bio-Medical to empower all zebrafish researchers. It allows true high-content imaging in zebrafish for the primary time.
Athena permits parameter-free zebrafish evaluation utilizing easy bright-field photos. It robotically detects zebrafish embryos and larvae as much as 5 days previous (dpf), extracting the fish contour and far of its inner anatomy (yolk sac, eye, notocord, and extra), together with physique areas of the top, trunk, and tail.
For every of those objects, the software program measures the morphology (space, size, and form) and might detect fluorescence in related shade channels. Both fluorescence depth and spot/construction detection inside particular anatomy are supported.
The software program is fitted to a broad vary of researchers and accepts a number of picture format varieties output from practically all microscope producers.
Click right here for a free 14-day trial of Athena Zebrafish software program, obtainable for obtain from the IDEA Bio-Medical web site.
What benefits does this methodology have over different methods?
Athena is the one automated software program devoted to zebrafish microscopy, providing a number of benefits:
- Automation: It permits experimental scale-up whereas eliminating subjective human bias or error and allowing direct comparability of outcomes between totally different labs.
- Intuitive and user-friendly interface: Users can rapidly and simply adapt Athena for his or her analysis.
- Versatile and versatile AI: Widely relevant for a lot of forms of screens involving zebrafish, as described by Athena prospects on the IDEA Bio-Medical YouTube web page.
- Customer help with personalised new consumer onboarding to make sure the success of our prospects.
What is the Flexible Pay-Per-Use license you might be providing, and what are its benefits?
IDEA Bio-Medical acknowledges that annual software program licenses might be costly, particularly if photos usually are not constantly analyzed all year long. Hence, we provide Athena on a pay-per-use foundation in order that zebrafish researchers can adapt their license to investigate photos after they want it.
We supply three inexpensive packages for various throughput wants. With an efficient value between $0.15 and $0.29 USD per picture, any Zebrafish lab or researcher can use Athena and improve their evaluation workflows.
Licenses might be bought month-to-month or quarterly, in response to want. This flexibility permits labs to regulate their licenses to suit their altering tasks, college students, grant submissions and different dynamics of educational analysis.
Source: IDEA Bio-Medical Ltd.
What help does IDEA Bio-Medical present to Athena software program customers?
Analyzing microscopy photos is advanced, requiring ability and expertise. Along with an intuitive software program interface, we provide personalised buyer help to allow any consumer of any ability degree to develop into unbiased and productive with Athena.
We at IDEA Bio-Medical take delight in working intently with our shoppers and their distinctive wants. New customers can obtain a one-on-one onboarding session with a certified product specialist to stroll by way of the software program utilizing their very own information and guarantee a easy, constructive first expertise.
Additional Athena help can also be obtainable by reaching out to IDEA Bio-Medical straight.
What is the longer term path of your Athena software program, and who would profit from utilizing it?
Athena is a wealthy application-based picture evaluation software program for straightforward and fast evaluation of microscope photos. The full Athena bundle is at present built-in into the Hermes platform, IDEA Bio-Medical’s flagship excessive content material screening (HCS) microscope.
In the longer term, the total Athena software program, related for microscopy photos of 2D and 3D cell tradition, shall be provided as a stand-alone platform, permitting all biology researchers to carry out picture evaluation on the push of a button.
About Dr. Otterstrom
Dr. Otterstrom obtained a Bachelor of Arts in Applied Physics on the University of Utah. As a Ph.D. pupil at Harvard University, he studied the biophysics of membrane fusion as mediated by influenza virus hemagglutinin protein utilizing single-molecule microscopy methods. He went on to acquire a Marie Curie fellowship to make the most of super-resolution imaging to review chromatin fine-packing buildings on the Institute of Photonic Sciences (ICFO) close to Barcelona, Spain.
As an software scientist for IDEA Bio-Medical, he helps shoppers with adapting their numerous experiments and assays to be carried out within the context of automated microscopy on the corporate’s flagship product, the WiScan Hermes.
About IDEA Bio-Medical Ltd.
IDEA Bio-Medical was based in 2007 by way of a partnership between YEDA (the Weizmann Institute’s commercialization arm) and IDEA Machine Development (an innovation hub).
The firm makes a speciality of automated imaging techniques and picture evaluation software program, providing a broad vary of organic functions primarily based on the corporate’s distinctive algorithms library.
The WiScan Hermes system incorporates essentially the most superior applied sciences at present obtainable within the machine imaginative and prescient area, built-in with engineering methodologies of excessive reliability and high quality on the degree of semi-conductors and digital printing industries, that are the specialty of the mom firm, IDEA Machine Development Design and Production Ltd.